Function type overview

Function in Spectre are grouped by the function prefix:

package.Functions that relate to managing the Spectre package and related dependencies. e.g. package.check().
read.Functions that read files into R. e.g. read.files().
do.Functions that manipulate or modify data, such as filtering or subsampling. e.g. do.subsample().
run.Functions that run an analytical process, such as FlowSOM or UMAP. e.g. run.umap().
make.Functions that create a data or visual output that is saved to disk. e.g. make.colour.plot().
write.Functions that write data to disk. e.g. write.files().

Spectre and other package loading/management

TaskCommand (with minimum variable inputs)
Load Spectre and other packages
## Load Spectre

## Check if required packages are loaded

## Load required packages
Set working directory to the location of your script, and saves this location as 'PrimaryDirectory'
### Set working directory
dirname(rstudioapi::getActiveDocumentContext()$path)            # Finds the directory where this script is located
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))     # Sets the working directory to where the script is located
PrimaryDirectory <- getwd()

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